Base Contrast Axis¶
The Base axis represents the fundamental tissue contrast weighting of an MRI series. It answers the question: "What physical contrast mechanism is this image based on?"
Overview¶
Base contrast is determined by the MRI physics parameters (TR, TE, TI) and acquisition type. Each base contrast emphasizes different tissue properties:
| Base | Full Name | Primary Signal | Clinical Use |
|---|---|---|---|
| T1w | T1-weighted | Short TR/TE, WM bright | Anatomy, Gd enhancement |
| T2w | T2-weighted | Long TR/TE, fluid bright | Pathology detection |
| PDw | Proton density | Long TR, short TE | Tissue composition |
| T2*w | T2-star weighted | GRE, susceptibility | Iron, blood products |
| DWI | Diffusion-weighted | Water motion | Stroke, tumors |
| PWI | Perfusion-weighted | Blood flow | Hemodynamics |
| SWI | Susceptibility-weighted | Phase + magnitude | Veins, microbleeds |
| MTw | Magnetization transfer | Bound protons | Myelin integrity |
| T1rho | T1-rho weighted | Spin-lock | Cartilage, research |
Detection Strategy¶
NILS uses a four-tier detection approach (in priority order):
Tier 1: Technique Inference¶
Some pulse sequences physics-lock to a specific base contrast:
| Technique | Implied Base | Confidence |
|---|---|---|
| MPRAGE, MEMPRAGE, MP2RAGE | T1w | 95% |
| TOF-MRA | T1w | 90% |
| ME-GRE, comb-ME-GRE | T2*w | 85-90% |
| SWI | SWI | 95% |
| DWI-EPI | DWI | 95% |
| ASL-EPI, DSC-EPI | PWI | 90-95% |
Why? These techniques have physics constraints that determine contrast. MPRAGE always has T1-weighting due to its IR-prepared 3D GRE design.
Tier 2: Exclusive Flags¶
Definitive signals from unified_flags that immediately identify base:
DWI indicators:
- is_dwi - Diffusion sequence flag
- has_adc - ADC map present
- has_fa - FA map present
- has_trace - Trace diffusion
PWI indicators:
- is_perfusion - Perfusion flag
- is_asl - Arterial spin labeling
- has_cbf, has_cbv, has_mtt, has_tmax, has_ttp - Perfusion maps
SWI indicators:
- is_swi - SWI sequence
- has_swi - SWI processing
MTw indicator:
- has_mtc - Magnetization transfer contrast
Synthetic MRI outputs:
- has_t1_synthetic → T1w
- has_t2_synthetic → T2w
- has_flair_synthetic → T2w (FLAIR base)
- has_pd_synthetic → PDw
Tier 3: Keyword Matching¶
Text search in series description for explicit contrast labels:
| Keywords | Base |
|---|---|
t1w, t1 weighted, t1-w |
T1w |
t2w, t2 weighted, t2-w |
T2w |
pdw, proton density |
PDw |
t2*, t2star |
T2*w |
dwi, diffusion, dti |
DWI |
pwi, perfusion, dsc, dce |
PWI |
swi, swan, venobold |
SWI |
mtw, magnetization transfer |
MTw |
Tier 4: Physics-Based Inference¶
When other methods fail, use TR/TE/TI thresholds (validated against 400K+ fingerprints):
Spin Echo (SE) Family¶
| Contrast | TR | TE | Notes |
|---|---|---|---|
| T1w | < 1000ms | < 30ms | Short TR/TE |
| T2w | > 2000ms | > 50ms | Long TR/TE |
| PDw | > 2000ms | < 30ms | Long TR, short TE |
Gradient Echo (GRE) Family¶
| Contrast | TE | Notes |
|---|---|---|
| T1w | < 10ms | Short TE |
| T2*w | > 15ms | Long TE for susceptibility |
Inversion Recovery (IR) Family¶
| Contrast | TI | Notes |
|---|---|---|
| T1w (standard IR) | 300-1500ms | Medium TI |
| T2w (STIR-like) | < 300ms | Short TI nulls fat |
Special Cases¶
FLAIR Differentiation¶
FLAIR can be T1-FLAIR or T2-FLAIR, differentiated by TE:
| Type | TE Threshold | Base | Typical Use |
|---|---|---|---|
| T1-FLAIR | < 40ms | T1w | Research |
| T2-FLAIR | ≥ 40ms | T2w | Clinical (most common) |
Database validation shows: - 97% of series with "t1" keyword + FLAIR have TE < 40ms - 99.9% of series with "t2" keyword + FLAIR have TE ≥ 80ms
FLAIR Modifier
The FLAIR modifier is detected on the Modifier axis separately. Here we only determine the underlying base contrast (T1w vs T2w).
Dual-Echo PD+T2¶
Dual-echo sequences acquire both PD and T2 in a single acquisition. NILS splits these into separate stacks and uses TE to determine which echo:
| Echo Type | TE | Base |
|---|---|---|
| PD echo | < 40ms | PDw |
| T2 echo | ≥ 40ms | T2w |
Detection triggers when BOTH "pd" and "t2" keywords appear in the series description.
MP2RAGE Outputs¶
MP2RAGE is fundamentally a T1-weighted technique. All outputs receive T1w base:
| Output | Flags | Base |
|---|---|---|
| INV1 | is_mp2rage_inv1 |
T1w |
| INV2 | is_mp2rage_inv2 |
T1w |
| UNI | has_uniform |
T1w |
| UNI-DEN | is_uniform_denoised |
T1w |
| T1 Map | has_t1_map |
T1w |
Quantitative Maps¶
Relaxometry maps have an implied base from their measurement:
| Map | Base | Rationale |
|---|---|---|
| T1 Map, R1 | T1w | Measures T1 relaxation |
| T2 Map, R2 | T2w | Measures T2 relaxation |
Primary Tissue Contrasts¶
T1w (T1-Weighted)¶
Physics: Short TR (~500-800ms) allows incomplete T1 recovery, emphasizing T1 differences. Short TE (~10-20ms) minimizes T2 effects.
Signal characteristics: - White matter: bright (short T1) - Gray matter: intermediate - CSF: dark (long T1) - Fat: bright
Clinical applications: - Anatomy reference - Gadolinium enhancement - Post-contrast lesion detection
T2w (T2-Weighted)¶
Physics: Long TR (>2000ms) allows full T1 recovery, eliminating T1 contrast. Long TE (>50ms) emphasizes T2 differences.
Signal characteristics: - White matter: dark - Gray matter: intermediate - CSF: very bright (long T2) - Edema: bright
Clinical applications: - Pathology detection - MS lesions - Tumor visualization - Infection/inflammation
PDw (Proton Density)¶
Physics: Long TR (>2000ms) removes T1 contrast. Short TE (<30ms) minimizes T2 contrast. Signal primarily reflects hydrogen density.
Signal characteristics: - Intermediate contrast - CSF: bright - Tissues differentiated by proton content
Clinical applications: - Often paired with T2w (dual-echo) - Cartilage imaging - Research applications
T2*w (T2-Star Weighted)¶
Physics: GRE sequence without 180° refocusing pulse. Sensitive to microscopic field inhomogeneities (susceptibility effects).
Signal characteristics: - Blood products: dark (paramagnetic) - Iron deposits: dark - Calcium: dark - Air-tissue interfaces: signal dropout
Clinical applications: - Hemorrhage detection - Microbleed identification - Iron quantification - Basis for SWI and BOLD
Specialized Contrasts¶
DWI (Diffusion-Weighted)¶
Physics: Measures random motion of water molecules using diffusion gradients. Contrast depends on b-value.
Signal characteristics: - Restricted diffusion: bright (acute stroke) - Free water: dark - High b-value → more diffusion weighting
Derived maps: - ADC (Apparent Diffusion Coefficient) - FA (Fractional Anisotropy) - MD (Mean Diffusivity) - Trace
PWI (Perfusion-Weighted)¶
Physics: Measures blood flow dynamics. Multiple methods: - DSC: Dynamic susceptibility contrast (T2-based) - DCE: Dynamic contrast-enhanced (T1-based) - ASL*: Arterial spin labeling (non-contrast)
Outputs: - CBF (Cerebral Blood Flow) - CBV (Cerebral Blood Volume) - MTT (Mean Transit Time) - Tmax, TTP (time parameters)
SWI (Susceptibility-Weighted)¶
Physics: Combines GRE magnitude and filtered phase images to enhance susceptibility contrast.
Signal characteristics: - Paramagnetic substances: very dark - Veins: dark (deoxyhemoglobin) - Superior to T2* for small structures
Applications: - Microbleed detection - Venous imaging - Iron quantification - QSM derivation
MTw (Magnetization Transfer)¶
Physics: Off-resonance RF pulse saturates bound (macromolecular) protons. Saturation transfers to free water pool, reducing signal in tissues with bound protons.
Signal characteristics: - Myelin-rich tissue: signal loss - Free water: minimal effect
Applications: - MS lesion characterization - Myelin integrity assessment
Confidence Levels¶
Detection confidence varies by method:
| Method | Confidence | Rationale |
|---|---|---|
| Technique inference | 95% | Physics-locked |
| Exclusive flags | 90% | Definitive markers |
| Keywords | 85% | Text-based |
| FLAIR/Dual-echo TE | 85% | Physics threshold |
| Physics ranges | 70% | Edge case fallback |
| Unknown fallback | 50% | Could not determine |
Conflict Detection¶
NILS checks for conflicts between detection method and text evidence:
- If physics predicts T1w but text contains "t2w" → conflict flagged
- Conflicts trigger manual review
- Authoritative methods (technique inference, exclusive flags) skip conflict check
YAML Configuration¶
Base detection is configured in backend/src/classification/detection_yaml/base-detection.yaml:
bases:
T1w:
name: "T1w"
description: "T1-weighted; short TR/TE, white matter bright"
keywords:
- "t1w"
- "t1 weighted"
physics:
se:
tr_max: 1000
te_max: 30
gre:
te_max: 10
technique_inference:
MPRAGE: ["T1w", 0.95]
MP2RAGE: ["T1w", 0.95]
# ...
rules:
allow_multiple: false # Only one base per series
priority_order:
- "DWI"
- "PWI"
- "SWI"
# ... (specialized first, then primary)